* Reverted r2535 except for changes to scripts/perl/Makefile.PL

* scripts/openbabel-python.i: Updated SWIG interface file to ignore 21 methods of each std::vector created. This should substantially reduce the size of the wrapper code
2025-02-25 18:55:23 -06:00 · 2008-06-17 19:03:50 +00:00
parent 5b53678b4d
commit 625a89e365
8 changed files with 123 additions and 232 deletions
--- a/7
+++ b/7
@@ -1,3 +1,10 @@
+2008-06-17  Noel O'Boyle  <baoilleach@gmail.com>
+
+	* Reverted r2535 except for changes to scripts/perl/Makefile.PL
+	* scripts/openbabel-python.i: Updated SWIG interface file to ignore 21
+	methods of each std::vector created. This should substantially reduce
+	the size of the wrapper code.
+
 2008-06-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

 	* src/formats/xtcformat.cpp: make confs a std::vector too. Was double
--- a/scripts/Makefile.am
+++ b/scripts/Makefile.am
@@ -20,9 +20,8 @@ dist-hook:

 if MAINTAINER_MODE
 if BUILD_SWIG
-BUILT_SOURCES = perl/openbabel_perl.cpp \
-	java/openbabel_java.cpp csharp/openbabel_csharp.cpp \
-	python/obcore.cpp python/obconversion.cpp python/obtemplate.cpp
+BUILT_SOURCES = perl/openbabel_perl.cpp python/openbabel_python.cpp \
+	java/openbabel_java.cpp csharp/openbabel_csharp.cpp

 script_includes = $(top_srcdir)/include/openbabel
 script_headers = $(script_includes)/mol.h $(script_includes)/obconversion.h \
@@ -35,17 +34,19 @@ perl/openbabel_perl.cpp: openbabel-perl.i $(script_headers)
 	sed -e "s/^@EXPORT.*/& sub dl_load_flags { 0x01 }/" <perl/OpenBabel.pm >perl/OpenBabel.new;
 	mv perl/OpenBabel.new perl/OpenBabel.pm;

-python/obconversion.cpp: openbabel-python2.i $(script_headers)
-	$(SWIG) -small -O -python -templatereduce -naturalvar \
-		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
-
-python/obtemplate.cpp: openbabel-python3.i $(script_headers)
-	$(SWIG) -small -O -python -templatereduce -naturalvar \
-		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
-
-python/obcore.cpp: openbabel-python.i $(script_headers)
+python/openbabel_python.cpp: openbabel-python.i $(script_headers)
 	$(SWIG) -small -O -python -templatereduce -naturalvar \
 		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
+	echo "import sys" >python/ob.py;
+	echo "if sys.platform.find(\"linux\") != -1:"  >>python/ob.py;
+	echo "    try:" >>python/ob.py;
+	echo "        import dl" >>python/ob.py;
+	echo "    except ImportError:" >>python/ob.py;
+	echo "        import DLFCN as dl" >>python/ob.py;
+	echo "    sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >>python/ob.py;
+	echo >>python/ob.py;
+	cat python/openbabel.py >>python/ob.py;
+	mv python/ob.py python/openbabel.py;

 java/openbabel_java.cpp: openbabel-java.i $(script_headers)
 	$(SWIG) -small -O -java -naturalvar -templatereduce -c++ -o $@ \
--- a/scripts/Makefile.in
+++ b/scripts/Makefile.in
@@ -34,12 +34,8 @@ host_triplet = @host@
 subdir = scripts
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/autoconf/libtool.m4 \
-	$(top_srcdir)/autoconf/ltoptions.m4 \
-	$(top_srcdir)/autoconf/ltsugar.m4 \
-	$(top_srcdir)/autoconf/ltversion.m4 \
-	$(top_srcdir)/autoconf/lt~obsolete.m4 \
-	$(top_srcdir)/acinclude.m4 $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
+	$(top_srcdir)/configure.in
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
@@ -93,7 +89,6 @@ LIBDL = @LIBDL@
 LIBOBJS = @LIBOBJS@
 LIBS = @LIBS@
 LIBTOOL = @LIBTOOL@
-LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
 MAINT = @MAINT@
@@ -103,8 +98,6 @@ NM = @NM@
 NMEDIT = @NMEDIT@
 OBJDUMP = @OBJDUMP@
 OBJEXT = @OBJEXT@
-OTOOL = @OTOOL@
-OTOOL64 = @OTOOL64@
 PACKAGE = @PACKAGE@
 PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
@@ -180,7 +173,6 @@ sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
 sysconfdir = @sysconfdir@
 target_alias = @target_alias@
-top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 EXTRA_DIST = openbabel-perl.i perl \
@@ -193,11 +185,9 @@ EXTRA_DIST = openbabel-perl.i perl \
 # build the scripting language interfaces if --enable-maintainer-mode was set
 # and SWIG is available -- please use the most recent version of SWIG
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@BUILT_SOURCES = perl/openbabel_perl.cpp \
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	python/openbabel_python.cpp \
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	java/openbabel_java.cpp \
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	csharp/openbabel_csharp.cpp \
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	python/obcore.cpp \
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	python/obconversion.cpp \
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	python/obtemplate.cpp \
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(am__append_1)
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@script_includes = $(top_srcdir)/include/openbabel
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@script_headers = $(script_includes)/mol.h $(script_includes)/obconversion.h \
@@ -396,17 +386,19 @@ dist-hook:
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	sed -e "s/^@EXPORT.*/& sub dl_load_flags { 0x01 }/" <perl/OpenBabel.pm >perl/OpenBabel.new;
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	mv perl/OpenBabel.new perl/OpenBabel.pm;

-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/obconversion.cpp: openbabel-python2.i $(script_headers)
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(SWIG) -small -O -python -templatereduce -naturalvar \
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
-
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/obtemplate.cpp: openbabel-python3.i $(script_headers)
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(SWIG) -small -O -python -templatereduce -naturalvar \
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
-
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/obcore.cpp: openbabel-python.i $(script_headers)
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/openbabel_python.cpp: openbabel-python.i $(script_headers)
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(SWIG) -small -O -python -templatereduce -naturalvar \
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "import sys" >python/ob.py;
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "if sys.platform.find(\"linux\") != -1:"  >>python/ob.py;
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "    try:" >>python/ob.py;
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "        import dl" >>python/ob.py;
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "    except ImportError:" >>python/ob.py;
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "        import DLFCN as dl" >>python/ob.py;
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "    sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >>python/ob.py;
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo >>python/ob.py;
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	cat python/openbabel.py >>python/ob.py;
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	mv python/ob.py python/openbabel.py;

@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@java/openbabel_java.cpp: openbabel-java.i $(script_headers)
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(SWIG) -small -O -java -naturalvar -templatereduce -c++ -o $@ \
--- a/scripts/openbabel-python.i
+++ b/scripts/openbabel-python.i
@@ -1,4 +1,4 @@
-%module obcore
+%module openbabel

 %{
 // used to set import/export for Cygwin DLLs
@@ -41,6 +41,79 @@

 %}

+%include "std_list.i"
+%include "std_map.i"
+%include "std_vector.i"
+%include "std_string.i"
+
+namespace std {
+
+%define VVTEMPLATE_WRAP(name, T) 
+%feature("ignore") vector< vector<T> >::append;
+%feature("ignore") vector< vector<T> >::assign;
+%feature("ignore") vector< vector<T> >::back;
+%feature("ignore") vector< vector<T> >::begin;
+%feature("ignore") vector< vector<T> >::capacity;
+%feature("ignore") vector< vector<T> >::clear;
+%feature("ignore") vector< vector<T> >::empty;
+%feature("ignore") vector< vector<T> >::end;
+%feature("ignore") vector< vector<T> >::erase;
+%feature("ignore") vector< vector<T> >::front;
+%feature("ignore") vector< vector<T> >::get_allocator;
+%feature("ignore") vector< vector<T> >::insert;
+%feature("ignore") vector< vector<T> >::pop;
+%feature("ignore") vector< vector<T> >::pop_back;
+%feature("ignore") vector< vector<T> >::push_back;
+%feature("ignore") vector< vector<T> >::rbegin;
+%feature("ignore") vector< vector<T> >::rend;
+%feature("ignore") vector< vector<T> >::reserve;
+%feature("ignore") vector< vector<T> >::resize;
+%feature("ignore") vector< vector<T> >::size;
+%feature("ignore") vector< vector<T> >::swap;
+%template(vectorv ## name) vector< vector<T> >;
+%enddef
+
+%define VECTORTEMPLATE_WRAP(vectorname, T) 
+%feature("ignore") vector<T>::append;
+%feature("ignore") vector<T>::assign;
+%feature("ignore") vector<T>::back;
+%feature("ignore") vector<T>::begin;
+%feature("ignore") vector<T>::capacity;
+%feature("ignore") vector<T>::clear;
+%feature("ignore") vector<T>::empty;
+%feature("ignore") vector<T>::end;
+%feature("ignore") vector<T>::erase;
+%feature("ignore") vector<T>::front;
+%feature("ignore") vector<T>::get_allocator;
+%feature("ignore") vector<T>::insert;
+%feature("ignore") vector<T>::pop;
+%feature("ignore") vector<T>::pop_back;
+%feature("ignore") vector<T>::push_back;
+%feature("ignore") vector<T>::rbegin;
+%feature("ignore") vector<T>::rend;
+%feature("ignore") vector<T>::reserve;
+%feature("ignore") vector<T>::resize;
+%feature("ignore") vector<T>::size;
+%feature("ignore") vector<T>::swap;
+%template(vector ## vectorname) vector<T>;
+%enddef
+
+VECTORTEMPLATE_WRAP(Int, int)
+VECTORTEMPLATE_WRAP(UnsignedInt, unsigned int)
+VVTEMPLATE_WRAP(Int, int)
+VECTORTEMPLATE_WRAP(Double, double)
+VECTORTEMPLATE_WRAP(String, std::string)
+VECTORTEMPLATE_WRAP(Vector3, OpenBabel::vector3)
+VECTORTEMPLATE_WRAP(OBMol, OpenBabel::OBMol)
+VECTORTEMPLATE_WRAP(OBBond, OpenBabel::OBBond)
+VECTORTEMPLATE_WRAP(OBResidue, OpenBabel::OBResidue)
+VECTORTEMPLATE_WRAP(OBRing, OpenBabel::OBRing)
+VECTORTEMPLATE_WRAP(pOBRing, OpenBabel::OBRing*)
+VECTORTEMPLATE_WRAP(pOBGenericData, OpenBabel::OBGenericData*)
+
+}
+
+
 %inline %{
 OpenBabel::OBPairData *toPairData(OpenBabel::OBGenericData *data) {
 	return (OpenBabel::OBPairData *) data;
@@ -73,11 +146,11 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 //# %import <openbabel/bitvec.h>
 %import <openbabel/typer.h>

-%import <openbabel/plugin.h>
+%include <openbabel/plugin.h>

-%import <openbabel/oberror.h>
-%import <openbabel/format.h>
-%import <openbabel/obconversion.h>
+%include <openbabel/oberror.h>
+%include <openbabel/format.h>
+%include <openbabel/obconversion.h>
 %include <openbabel/residue.h>
 %include <openbabel/internalcoord.h>
 %include <openbabel/atom.h>
@@ -88,11 +161,11 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %include <openbabel/alias.h>
 %include <openbabel/atomclass.h>

-%import <openbabel/fingerprint.h>
-%import <openbabel/descriptor.h>
-%import <openbabel/forcefield.h>
+%include <openbabel/fingerprint.h>
+%include <openbabel/descriptor.h>
+%include <openbabel/forcefield.h>

-%import <openbabel/op.h>
+%include <openbabel/op.h>

 %include <openbabel/bitvec.h>

--- a/scripts/openbabel-python2.i
+++ b/scripts/openbabel-python2.i
@@ -1,92 +0,0 @@
-%module obconversion
-
-%{
-// used to set import/export for Cygwin DLLs
-#ifdef WIN32
-#define USING_OBDLL
-#endif
-
-#include <openbabel/base.h>
-
-#include <openbabel/generic.h>
-#include <openbabel/griddata.h>
-#include <openbabel/math/vector3.h>
-#include <openbabel/bitvec.h>
-
-#include <openbabel/mol.h>
-#include <openbabel/obconversion.h>
-#include <openbabel/oberror.h>
-#include <openbabel/plugin.h>
-#include <openbabel/fingerprint.h>
-#include <openbabel/descriptor.h>
-#include <openbabel/format.h>
-#include <openbabel/forcefield.h>
-#include <openbabel/op.h>
-
-%}
-
-// These methods are renamed to valid Python method names, as otherwise
-// they cannot be used from Python
-%rename(inc)   *::operator++;
-%rename(good)  *::operator bool;
-
-%import <openbabel/babelconfig.h>
-
-%import <openbabel/base.h>
-%import <openbabel/generic.h>
-%import <openbabel/griddata.h>
-
-%import <openbabel/math/vector3.h>
-%import <openbabel/bitvec.h>
-
-%import <openbabel/chains.h>
-%import <openbabel/typer.h>
-
-%include <openbabel/plugin.h>
-%include <openbabel/oberror.h>
-%include <openbabel/format.h>
-%include <openbabel/obconversion.h>
-%import <openbabel/residue.h>
-%import <openbabel/internalcoord.h>
-%import <openbabel/atom.h>
-%import <openbabel/bond.h>
-%import <openbabel/mol.h>
-%import <openbabel/ring.h>
-%import <openbabel/parsmart.h>
-
-%include <openbabel/fingerprint.h>
-%include <openbabel/descriptor.h>
-%include <openbabel/forcefield.h>
-
-%include <openbabel/op.h>
-%include <openbabel/bitvec.h>
-
-%ignore *::operator=;
-
-%include "carrays.i"
-%array_class(double, doubleArray)
-%pythoncode %{
-def double_array(mylist):
-    """Create a C array of doubles from a list."""
-    c = doubleArray(len(mylist))
-    for i,v in enumerate(mylist):
-        c[i] = v
-    return c
-%}
-
-# Functions to set the log file to std::cout and std::cerr
-       
-%ignore OBForceField::SetLogFile(std::ostream *pos);
-%extend OpenBabel::OBForceField {
-  void SetLogToStdOut() 
-  {
-    self->SetLogFile(&std::cout);
-  }
-
-  void SetLogToStdErr() 
-  {
-    self->SetLogFile(&std::cerr);
-  }
-};    
-
-
--- a/scripts/openbabel-python3.i
+++ b/scripts/openbabel-python3.i
@@ -1,65 +0,0 @@
-%module obtemplate
-
-%{
-// used to set import/export for Cygwin DLLs
-#ifdef WIN32
-#define USING_OBDLL
-#endif
-
-#include <openbabel/base.h>
-#include <openbabel/mol.h>
-#include <openbabel/atom.h>
-#include <openbabel/bond.h>
-#include <openbabel/residue.h>
-#include <openbabel/ring.h>
-
-%}
-
-%include "std_list.i"
-%include "std_map.i"
-%include "std_vector.i"
-%include "std_string.i"
-
-namespace std {
-%template (vectorInt)		  vector<int>;
-%template (vectorUnsignedInt)     vector<unsigned int>;
-%template (vvInt)		      vector< vector<int> >;
-%template (vectorDouble) 	vector<double>;
-%template (vectorString)		  vector<std::string>;
-%template (vVector3)		  vector<OpenBabel::vector3>;
-
-%template (vectorMol)		  vector<OpenBabel::OBMol>;
-%template (vectorBond)		vector<OpenBabel::OBBond>;
-%template (vectorResidue)	vector<OpenBabel::OBResidue>;
-%template (vectorRing)		vector<OpenBabel::OBRing>;
-%template (vectorpRing)		vector<OpenBabel::OBRing*>;
-%template (vectorData)    vector<OpenBabel::OBGenericData*>;
-}
-
-// These methods are renamed to valid Python method names, as otherwise
-// they cannot be used from Python
-%rename(inc)   *::operator++;
-%rename(good)  *::operator bool;
-
-%import <openbabel/babelconfig.h>
-
-%import <openbabel/base.h>
-%import <openbabel/residue.h>
-%import <openbabel/atom.h>
-%import <openbabel/bond.h>
-%import <openbabel/mol.h>
-%import <openbabel/ring.h>
-
-%ignore *::operator=;
-
-%include "carrays.i"
-%array_class(double, doubleArray)
-%pythoncode %{
-def double_array(mylist):
-    """Create a C array of doubles from a list."""
-    c = doubleArray(len(mylist))
-    for i,v in enumerate(mylist):
-        c[i] = v
-    return c
-%}
-
--- a/scripts/python/openbabel.py
+++ b/scripts/python/openbabel.py
@@ -1,11 +0,0 @@
-import sys
-if sys.platform.find("linux") != -1:
-    try:
-        import dl
-    except ImportError:
-        import DLFCN as dl
-    sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
-
-import obcore
-import obconversion
-import obtemplate
--- a/scripts/python/setup.py
+++ b/scripts/python/setup.py
@@ -60,22 +60,8 @@ def find_likely_directory():

 OBinclude,OBlibrary = find_likely_directory()

-obCore = Extension('_obcore',
-                   ['obcore.cpp'],
-                   include_dirs=OBinclude,
-                   library_dirs=OBlibrary,
-                   libraries=['openbabel']
-                   )
-
-obConversion = Extension('_obconversion',
-                         ['obconversion.cpp'],
-                         include_dirs=OBinclude,
-                         library_dirs=OBlibrary,
-                         libraries=['openbabel']
-                         )
-
-obTemplate = Extension('_obtemplate',
-                       ['obtemplate.cpp'],
+obExtension = Extension('_openbabel',
+                        ['openbabel_python.cpp'],
                        include_dirs=OBinclude,
                        library_dirs=OBlibrary,
                        libraries=['openbabel']
@@ -88,7 +74,7 @@ setup(name='openbabel',
      url='http://openbabel.sourceforge.net/',
      license='http://www.gnu.org/copyleft/gpl.html',
      py_modules=['openbabel','pybel'],
-      ext_modules=[obCore, obConversion, obTemplate],
+      ext_modules=[obExtension],
      description = 'openbabel: Python interface to the Open Babel chemistry library',
      classifiers=[
      'Development Status :: 5 - Production/Stable',